<code>xrdb -load</code> loads the relevant configuration resource. <code>xrdb -merge</code> sorts, and in some cases prioritizes, said configurations, hence why I saw <code>-merge</code> as the culprit for <code>gdm</code> ignoring my .Xdefaults. (Perhaps <code>-override -retain</code> might have been more suitable.)

Having said that, it seems I have been living in the past. Fedora now uses (deprecating .Xdefaults?) .Xresources, ie $sysresources points to .Xresources through the new xinitrc-common file (instead of the old gdm/Init/Default) and explicitly includes $HOME/.Xresources.

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